rs1942043

Variant names:

• chr2-134797922-T-C
• rs1942043
• ENST00000392929.6:n.427-62341A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392929.6(CCNT2-AS1):​n.427-62341A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,278 control chromosomes in the GnomAD database, including 292 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.049 (292 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCNT2-AS1 ENST00000392929.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

CCNT2-AS1 (HGNC:40130): (CCNT2 antisense RNA 1)

VDAC2P4 (HGNC:51932): (VDAC2 pseudogene 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNT2-AS1	ENST00000392929.6	n.427-62341A>G		intron_variant	Intron 3 of 3	4
VDAC2P4	ENST00000452925.1	n.*43T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7449 AN: 152160 Hom.: 288 Cov.: 32

Gnomad AFR AF: 0.0655

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0615

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0516

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0491 AC: 7478 AN: 152278 Hom.: 292 Cov.: 32 AF XY: 0.0508 AC XY: 3780 AN XY: 74478

Gnomad4 AFR AF: 0.0658

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0615

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0207

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0310 Hom.: 35

Bravo AF: 0.0569

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1942043; hg19: chr2-135555492;